GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gdh in Dinoroseobacter shibae DFL-12

Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate 3608118 Dshi_1523 glucose sorbosone dehydrogenase (RefSeq)

Query= BRENDA::I7A144
         (352 letters)



>FitnessBrowser__Dino:3608118
          Length = 369

 Score =  155 bits (391), Expect = 2e-42
 Identities = 114/351 (32%), Positives = 166/351 (47%), Gaps = 40/351 (11%)

Query: 21  LRVEEVVGGLEVPWALAFLPDGGMLIAERPGRIRLFR-EGRLSTYAELP-VYHRGESGLL 78
           + V+E+V  L+ PWA  FLP+GG+LI ER G +   R +G  +  + LP +   G+ GLL
Sbjct: 31  VEVKEIVRDLDEPWAFGFLPEGGVLITERGGALLHIRPDGTRTEVSGLPRIAVGGQGGLL 90

Query: 79  GLALHPRFPEA-PYVYAYRTVAEGGLRNQVVRLRHLGERGVLD--RVVLDGIPARPHGLH 135
            L +   F +    V++Y      G    V   R   +   L+  R +         G H
Sbjct: 91  DLLIPADFAQTREVVFSYSRPQARGAGTAVAVGRFSADGRALENTRTIFAMEEGTRGGRH 150

Query: 136 SGGRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGARPE 195
            G RI  G DG LYVT G+  + + AQ+LA   G ++R+  +G     NPF G  GA+PE
Sbjct: 151 FGSRIVEGRDGFLYVTIGDRGDDDSAQNLAIESGSVIRIARDGGIPTSNPFTGTEGAQPE 210

Query: 196 VYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRV------- 248
           ++S GHRNPQG A   + G L+  EHG       G DE+N +  G NYGWP +       
Sbjct: 211 IWSYGHRNPQGAALDLQ-GNLWVVEHG-----ARGGDEINRVEMGANYGWPVISYGRHYS 264

Query: 249 ---VGRGN-DPRYRDPLYFWPQGFPPGNLAFF--------RGDLYVAGLRGQALLRLVLE 296
              +G G   P    P +FW     P  +  +         GD +V  L+   L RL   
Sbjct: 265 GLRIGEGTAKPGMEQPAHFWDPSIAPSGMMIYSGALWPEWEGDFFVGSLKFGYLSRL--- 321

Query: 297 GERGRWRVLRVETALSG--FGRLREVQVGPDGALYVTTSNRDGRGQVRPGD 345
            E G +     E  ++G    RLR+V+ GPDGA++  +       ++ P +
Sbjct: 322 -EAGSF----AEEEITGDTTARLRDVREGPDGAIWFLSVGNGALYRMSPAE 367


Lambda     K      H
   0.322    0.146    0.460 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 489
Number of extensions: 31
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 352
Length of database: 369
Length adjustment: 29
Effective length of query: 323
Effective length of database: 340
Effective search space:   109820
Effective search space used:   109820
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory